Expression profiles analysis identifies a novel three-mRNA signature to predict overall survival in oral squamous cell carcinoma.

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Gene expression profiles of GSE13601, GSE30784, GSE37991 and The Cancer Genome Atlas (TCGA) head and neck cancer were downloaded from gene expression omnibus (GEO) and TCGA database respectively. R software and bioconductor packages were used to compare and identify the differentially expressed genes (DEGs) between OSCC tissues and normal controls. The common DEGs were then subjected to gene ontology (GO) enrichment analysis, ingenuity pathway analysis (IPA), protein-protein interaction (PPI) network analysis as well as survival analysis. A total of 76 up- and 102 down-regulated DEGs were identified. Functional analysis revealed that these DEGs were associates with increased oncostatin M signaling, cell diapedesis and extravasation as well as reduced calcium signaling and loss of adherens junctions and tight junctions. A set of robust prognostic signatures including PLAU, CLDN8 and CDKN2A were identified from DEGs and could predict overall survival in OSCC patients from TCGA cohort. This three-gene signature was further successfully validated as a prognostic marker for overall survival prediction in another independent cohort GSE41613. In conclusion, our study has identified a registry of novel genes and pathways that play important roles in regulating the initiation and development of OSCC. A set of robust molecular signature is identified for prognostic prediction, which will provide useful guidance for therapeutic applications.", "claims": [{"id": "claim-target-result", "statement": "Using R software and Bioconductor packages, the study compared OSCC tissues with normal controls across gene-expression data downloaded from GEO and TCGA and identified 76 up-regulated and 102 down-regulated differentially expressed genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29637000", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Gene expression profiles of GSE13601, GSE30784, GSE37991 and The Cancer Genome Atlas (TCGA) head and neck cancer were downloaded from gene expression omnibus (GEO) and TCGA database respectively. R software and bioconductor packages were used to compare and identify the differentially expressed genes (DEGs) between OSCC tissues and normal controls."}, {"asset": "source:pmid:29637000", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 76 up- and 102 down-regulated DEGs were identified."}], "state": "complete"}], "gaps": ["doi"]}, "experiment": {"state": "partial", "objective": "Using R software and Bioconductor packages, the study compared OSCC tissues with normal controls across gene-expression data downloaded from GEO and TCGA and identified 76 up-regulated and 102 down-regulated differentially expressed genes.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:29637000"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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